Construction of ancestral TRM states was performed using PastML (Ishikawa et al, 2019) with six methods, including three maximum parsimony ACCTRAN (accelerated transformation), DELTRAN (delayed transformation), and DOWNPASS, as well as three maximum likelihood methods JOINT, MAP (maximum a posteriori), and MPPA (marginal posterior probabilities approximation). The Newick tree file and TRM traits (TTAGG, absent, and novel) were provided as input.
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